Fixes for PaladinsGDX were necessary, otherwise the game would have been unplayable (head bobbing, infinite projectiles, jumping and most likely a few others I can't currently recall). Now, while 5th episode boss was shitty, I strongly disagree fixing him, as that would be altering the game way too much, too much for a port which is supposed to bring "vanilla" experience (yes, yes, sometimes M210 doesn't exactly follow that rule).

Not my project but I think the thing should be coded in as-is before doing any fixes like that. If it's a coding bug then it's part of the original gameplay.
7p's case is more about tweaking the game to play like it did with old machines back in the day, as the game didn't have limits for it's timers, liberties were taken instead to fix those timers to the same saner values that you'd see on slower hardware.
In this case it's more about fixing an oversight that only appeared later on.